I'm sticking with Ocarina of Time first, but I always wanted to play Yoshi's Story. In the second wave of games, I really want to play Paper Mario which I've never played besides some of the sequels. I will play Majora's Mask and Banjo Kazooie as well. Kirby 64 I only played once and look forward to completing.
The games that aren't currently planned that I want to see are Pokemon Stadium 1 and 2, Donkey Kong 64, Mystical Ninja Starring Goeman, and any of the Mario Parties. I was literally in the middle of a Mystical Ninja playthrough when my N64 starting freezing much more often earlier this year. Pokemon Stadiums are amazing for minigames and battles (would be the best multiplayer N64 game in my opinion), and it won't happen but would be amazing if Nintendo let us play Red, Blue, Yellow, Gold, Silver, and Crystal directly in our Pokemon Stadium files.